Knowledge Based Potentials for Predicting the Three-Dimensional Conformation of Proteins

Several potentials are derived from a data set of 75 non—homologous known protein structures by computing statistical relations between amino acid sequence and different descriptions of the protein conformation. These potentials formulate in different ways backbone dihedral angle preferences, pair—wise distance dependent interactions between amino acid residues and solvation effects based on accessible surface areas. Parameters affecting the characteristics and the performance of the potentials are critically assessed by monitoring the recognition of the native fold in a strict screening test, where each sequence in the data set is threaded through a repertoire of motifs, generated from all corresponding structures. For a detailed description of this analysis, the reader is referred to ref. 1; recent reviews on the subject can be found in refs. 2–4.